Retinal Reconstruction Program
Kernel estimate over grid
The deformation energy function
The deformation energy function
Piecewise smooth function used in area penalty
The deformation energy gradient function
Construct an outline object. This sanitises the input points P, as d...
The identity transformation
Read one of the Thompson lab's retinal datasets
Read a retinal dataset in IJROI format
Read a retinal dataset in IJROI format
Interpolate values in image
Invert sphere about its centre
Invert sphere to hemisphere
Karcher mean on the sphere
Find the optimal concentration for a set of data
Kernel density estimate on sphere using Fisherian density with Cartesi...
Kernel density estimate on sphere using Fisherian density with polar c...
Estimate of the log likelihood of the points mu given a particular val...
Find the optimal concentration for a set of data
Cross validation estimate of the least squares error of the points mu ...
Kernel regression on sphere using Fisherian density with Cartesian coo...
Kernel regression on sphere using Fisherian density with polar coordin...
Add point fullcuts to the outline
Read data counts in CSV format
Read data points in CSV format
Class containing functions and data to map CountSet s to Reconstructed...
Sinusoidal projection
Convert from Cartesian to dual-wedge coordinates
Convert from Cartesian to spherical coordinates
Convert from Cartesian to 'wedge' coordinates
Convert spherical coordinates on sphere to polar projection in Cartesi...
Convert from spherical to Cartesian coordinates
Area of triangles on a sphere
Convert from 'wedge' to Cartesian coordinates
Convert latitude on sphere to radial variable in area-preserving proje...
Spherical plot of reconstructed outline
Spherical plot of reconstructed outline
Class containing functions and data relating to Stitching outlines
Generate colours for strain plots
Stretch mesh
Area of triangles on a plane
"Signed area" of triangles on a plane
Class to triangulate Fragment s
Class containing functions and data relating to Triangulation
Retistruct UI
Vector norm
Plot flat TriangulatedOutline.
Determine indices of triangles that are flipped
Lambert azimuthal equal area projection
Azimuthal equidistant projection
Simplify an outline object by removing short edges
Convert barycentric coordinates of points in mesh on sphere to cartesi...
Central angle between two points on a sphere
Check the whether directory contains valid data
Return points on the unit circle
Determine indices of triangles that are flipped
Piecewise smooth function used in area penalty
Class containing functionality common to flat and reconstructed outlin...
Ancillary function to place labels
Arc length of a parabola y=x^2/4f
Inverse arc length of a parabola y=x^2/4f
Parse dependencies
Restore points to spherical manifold
Extract summary data for a batch of reconstructions
Retistruct check markup
Print a figure to file
Process a dataset, saving results to disk
Process a dataset with a time limit
Save reconstruction data in MATLAB format
Start the Retistruct GUI
Find the intersection of a plane with edges of triangles on a sphere
Class containing functions and data relating to annotating outlines
Convert azimuth-elevation coordinates to spherical coordinates
Azimuthal conformal or stereographic or Wulff projection
Subclass of FeatureSet to represent counts centred on points
Create grid on projection of hemisphere onto plane
Read a retinal dataset in CSV format
The deformation energy gradient function
Draw the "flat" outline in 3D with depth information
File system directories used by shinyFiles
Flat plot of reconstructed outline
Superclass containing functions and data relating to sets of features ...
Class containing functionality common to FeatureSets and `Reconstruc...
The FIRE algorithm
Flat plot of AnnotatedOutline
Flat plot of outline
Plot "flat" (unreconstructed) representation of outline
Flat plot of AnnotatedOutline
Subclass of FeatureSet to represent points
Determine intersection between two lines
Convert an list created by R6_to_list() into an R6 object.
List datasets underneath a directory
Plot the fractional change in length of mesh edges
Morph a flat dataset to a parabola for testing purposes
Return a new version of the list in which any unnamed elements have be...
Bring angle into range
Orthographic projection
Class containing basic information about flat outlines
Subclass of FeatureSet to represent points
Convert polar projection in Cartesian coordinates to spherical coordin...
Put text on the polar plot
Plot projection of a reconstructed outline
Projection of a reconstructed outline
Plot projection of reconstructed dataset
Convert an R6 object into a list, ignoring functions and environments
Class containing functions and data to map FeatureSet s to Reconstruct...
Class containing functions and data to map LandmarkSet s to Reconstruc...
Class containing functions to reconstruct StitchedOutline s and store ...
Class containing functions and data to map PointSet s to Reconstructed...
Remove identical consecutive rows from a matrix
Remove intersections between adjacent segments in a closed path
Reporting utility function
Read a retinal dataset
Class containing functions and data relating to retinal outlines
A version of ReconstructedOutline that is specific to retinal datasets
Export data from reconstruction data files to MATLAB
Plot figures for a batch of reconstructions
Get titrations from a directory of reconstructions
Plot titrations
Batch operation using the parallel package
Read the markup data
Read the reconstruction data from file
Reconstruct a retina
Save markup
Save reconstruction data
Rotate axis of sphere
Retistruct Shiny Server
Simplify an outline object by removing short edges
Reconstructs retinae by morphing a flat surface with cuts (a dissected flat-mount retina) onto a curvilinear surface (the standard retinal shape). It can estimate the position of a point on the intact adult retina to within 8 degrees of arc (3.6% of nasotemporal axis). The coordinates in reconstructed retinae can be transformed to visuotopic coordinates. For more details see Sterratt, D. C., Lyngholm, D., Willshaw, D. J. and Thompson, I. D. (2013) <doi:10.1371/journal.pcbi.1002921>.
Useful links